Genetic Diversity and Nodulation Potential of Bradyrhizobium Strains in Cowpea and Soybean

Bradyrhizobium is a genetically diverse genus that forms symbioses with numerous legumes, including major crops such as cowpea (Vigna unguiculata) and soybean (Glycine max). Understanding the genetic and symbiotic diversity of native strains is essential for improving inoculant technologies and enhancing biological nitrogen fixation in tropical agricultural systems. This study investigated Bradyrhizobium strains associated with these two legumes grown in adjacent tropical soils in Brazil to elucidate their genetic relationships, taxonomic placement, and host compatibility. A total of 34 Bradyrhizobium strains isolated from cowpea and soybean nodules were characterized using multilocus phylogenetic analyses (16S rRNA, gyrB, recA, and nodC). Selected strains underwent whole-genome sequencing for comparative analyses based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). Cross-inoculation assays were performed to evaluate nodulation capacity and symbiotic efficiency on both hosts. The strains displayed high genetic diversity, forming multiple phylogenetic clusters. Most grouped within the B. elkanii superclade, whereas several occupied divergent lineages, some potentially representing new taxa. Genome-based analyses supported these findings, showing intracluster ANI values above 95–96% and intercluster values below 94%. A distinct group of cowpea-derived strains exhibited high symbiotic efficiency but low genomic similarity to known type strains, suggesting the presence of a novel species with potential use in inoculants. In contrast, some soybean-derived strains were genetically identical to commercial inoculants, indicating persistence or re-isolation from previously inoculated soils. Notably, strain BR 13971, isolated from soybean, nodulated both hosts efficiently, demonstrating a broad host range and suggesting a unique symbiovar. Cross-inoculation assays showed that soybean-derived strains effectively nodulated cowpea, whereas cowpea-derived strains did not nodulate soybean, indicating asymmetrical host compatibility. Particularly for cowpea, strains BR 10926 and BR 10750 demonstrated higher symbiotic efficiency than the strains currently recommended for this crop. Overall, these findings enhance the understanding of Bradyrhizobium diversity in tropical soils and highlight promising native strains for future inoculant development.